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Fluorine in PDB 1nkk: Complex Structure of Hcmv Protease and A Peptidomimetic Inhibitor

Enzymatic activity of Complex Structure of Hcmv Protease and A Peptidomimetic Inhibitor

All present enzymatic activity of Complex Structure of Hcmv Protease and A Peptidomimetic Inhibitor:
3.4.21.97;

Protein crystallography data

The structure of Complex Structure of Hcmv Protease and A Peptidomimetic Inhibitor, PDB code: 1nkk was solved by R.Khayat, R.Batra, C.Qian, T.Halmos, M.Bailey, L.Tong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.98 / 2.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 105.170, 215.250, 52.330, 90.00, 90.00, 90.00
R / Rfree (%) 23.3 / 28

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Complex Structure of Hcmv Protease and A Peptidomimetic Inhibitor (pdb code 1nkk). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Complex Structure of Hcmv Protease and A Peptidomimetic Inhibitor, PDB code: 1nkk:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 1nkk

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Fluorine binding site 1 out of 12 in the Complex Structure of Hcmv Protease and A Peptidomimetic Inhibitor


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Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Complex Structure of Hcmv Protease and A Peptidomimetic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F265

b:21.5
occ:1.00
 FB1 E:CFT265 0.0 21.5 1.0
C1 E:CFT265 1.3 17.9 1.0
FB2 E:CFT265 2.1 19.4 1.0
FB3 E:CFT265 2.1 19.8 1.0
C E:ALA264 2.3 15.4 1.0
O E:ALA264 2.7 15.6 1.0
CA E:ALA264 2.9 16.0 1.0
CG A:ARG165 3.0 19.7 1.0
N A:ARG165 3.4 13.4 1.0
OG A:SER132 3.6 14.5 1.0
CB A:ARG165 3.8 16.9 1.0
O E:DMH263 3.8 17.3 1.0
CD A:ARG165 3.8 24.4 1.0
N E:ALA264 3.9 17.4 1.0
CB E:ALA264 4.1 15.2 1.0
NE A:ARG165 4.2 28.4 1.0
C E:DMH263 4.2 18.2 1.0
CA A:ARG165 4.2 14.8 1.0
CA A:GLY164 4.2 11.8 1.0
C A:GLY164 4.3 11.7 1.0
CB A:SER132 4.3 10.3 1.0
O A:VAL163 4.3 12.1 1.0
NE2 A:HIS63 4.8 5.3 1.0
O E:HOH2138 4.9 38.3 1.0

Fluorine binding site 2 out of 12 in 1nkk

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Fluorine binding site 2 out of 12 in the Complex Structure of Hcmv Protease and A Peptidomimetic Inhibitor


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Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Complex Structure of Hcmv Protease and A Peptidomimetic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F265

b:19.4
occ:1.00
 FB2 E:CFT265 0.0 19.4 1.0
C1 E:CFT265 1.3 17.9 1.0
FB1 E:CFT265 2.1 21.5 1.0
FB3 E:CFT265 2.1 19.8 1.0
C E:ALA264 2.4 15.4 1.0
O E:ALA264 2.8 15.6 1.0
OG A:SER132 2.9 14.5 1.0
CB A:SER132 3.0 10.3 1.0
SG A:CYS161 3.6 8.9 1.0
CA E:ALA264 3.8 16.0 1.0
NE2 A:HIS63 3.8 5.3 1.0
O A:VAL163 3.9 12.1 1.0
CD2 A:HIS63 3.9 8.0 1.0
CB A:CYS161 4.1 6.5 1.0
CA A:GLY164 4.3 11.8 1.0
N E:ALA264 4.4 17.4 1.0
O A:HOH2172 4.5 9.3 1.0
CA A:SER132 4.5 7.8 1.0
OD1 A:ASN62 4.6 15.8 1.0
N A:ARG165 4.7 13.4 1.0
C A:VAL163 4.8 10.1 1.0
CB E:ALA264 4.9 15.2 1.0
O E:DMH263 4.9 17.3 1.0
C E:DMH263 4.9 18.2 1.0

Fluorine binding site 3 out of 12 in 1nkk

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Fluorine binding site 3 out of 12 in the Complex Structure of Hcmv Protease and A Peptidomimetic Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Complex Structure of Hcmv Protease and A Peptidomimetic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F265

b:19.8
occ:1.00
 FB3 E:CFT265 0.0 19.8 1.0
C1 E:CFT265 1.3 17.9 1.0
FB2 E:CFT265 2.1 19.4 1.0
FB1 E:CFT265 2.1 21.5 1.0
C E:ALA264 2.4 15.4 1.0
OG A:SER132 2.9 14.5 1.0
NE2 A:HIS63 3.0 5.3 1.0
CA E:ALA264 3.0 16.0 1.0
O E:DMH263 3.0 17.3 1.0
N E:ALA264 3.1 17.4 1.0
CD2 A:HIS63 3.1 8.0 1.0
C E:DMH263 3.1 18.2 1.0
O E:ALA264 3.6 15.6 1.0
CB A:SER132 3.9 10.3 1.0
CB E:DMH263 4.0 17.3 1.0
CA E:DMH263 4.2 19.0 1.0
CE1 A:HIS63 4.2 8.0 1.0
CG A:HIS63 4.4 8.3 1.0
CB E:ALA264 4.5 15.2 1.0
CG A:ARG165 4.8 19.7 1.0
ND1 A:HIS63 5.0 8.6 1.0

Fluorine binding site 4 out of 12 in 1nkk

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Fluorine binding site 4 out of 12 in the Complex Structure of Hcmv Protease and A Peptidomimetic Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Complex Structure of Hcmv Protease and A Peptidomimetic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F565

b:20.9
occ:1.00
 FB1 F:CFT565 0.0 20.9 1.0
C1 F:CFT565 1.3 16.4 1.0
FB3 F:CFT565 2.1 18.2 1.0
FB2 F:CFT565 2.1 18.6 1.0
C F:ALA564 2.5 14.1 1.0
CA F:ALA564 2.9 14.1 1.0
O F:ALA564 3.1 12.1 1.0
CG B:ARG465 3.1 14.2 1.0
O F:DMH563 3.3 16.8 1.0
NE B:ARG465 3.6 19.7 1.0
OG B:SER432 3.6 13.0 1.0
N F:ALA564 3.7 14.9 1.0
CB B:ARG465 3.7 13.0 1.0
N B:ARG465 3.8 12.1 1.0
CD B:ARG465 3.8 18.1 1.0
C F:DMH563 3.9 16.4 1.0
O F:HOH2109 3.9 15.6 1.0
CB F:ALA564 4.1 14.0 1.0
CA B:ARG465 4.3 12.2 1.0
CB B:SER432 4.4 9.8 1.0
O F:HOH2225 4.5 20.3 1.0
C B:GLY464 4.6 10.3 1.0
CA B:GLY464 4.7 9.4 1.0
CZ B:ARG465 4.7 20.1 1.0
O B:VAL463 4.9 8.0 1.0
NE2 B:HIS363 4.9 2.3 1.0

Fluorine binding site 5 out of 12 in 1nkk

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Fluorine binding site 5 out of 12 in the Complex Structure of Hcmv Protease and A Peptidomimetic Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Complex Structure of Hcmv Protease and A Peptidomimetic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F565

b:18.6
occ:1.00
 FB2 F:CFT565 0.0 18.6 1.0
C1 F:CFT565 1.3 16.4 1.0
FB1 F:CFT565 2.1 20.9 1.0
FB3 F:CFT565 2.1 18.2 1.0
C F:ALA564 2.4 14.1 1.0
O F:ALA564 2.6 12.1 1.0
OG B:SER432 3.0 13.0 1.0
CB B:SER432 3.1 9.8 1.0
CA B:GLY464 3.6 9.4 1.0
O B:VAL463 3.7 8.0 1.0
SG B:CYS461 3.7 10.5 1.0
CA F:ALA564 3.7 14.1 1.0
N B:ARG465 4.0 12.1 1.0
C B:GLY464 4.2 10.3 1.0
CB B:CYS461 4.4 5.4 1.0
C B:VAL463 4.4 8.8 1.0
NE2 B:HIS363 4.4 2.3 1.0
N B:GLY464 4.4 8.9 1.0
CA B:SER432 4.5 8.4 1.0
N F:ALA564 4.5 14.9 1.0
CD2 B:HIS363 4.7 3.8 1.0
CG B:ARG465 4.7 14.2 1.0
CB F:ALA564 4.8 14.0 1.0
O F:HOH2225 4.8 20.3 1.0
O F:DMH563 4.9 16.8 1.0

Fluorine binding site 6 out of 12 in 1nkk

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Fluorine binding site 6 out of 12 in the Complex Structure of Hcmv Protease and A Peptidomimetic Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Complex Structure of Hcmv Protease and A Peptidomimetic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F565

b:18.2
occ:1.00
 FB3 F:CFT565 0.0 18.2 1.0
C1 F:CFT565 1.3 16.4 1.0
FB1 F:CFT565 2.1 20.9 1.0
FB2 F:CFT565 2.1 18.6 1.0
C F:ALA564 2.4 14.1 1.0
OG B:SER432 2.7 13.0 1.0
NE2 B:HIS363 2.9 2.3 1.0
CD2 B:HIS363 3.1 3.8 1.0
CA F:ALA564 3.1 14.1 1.0
N F:ALA564 3.3 14.9 1.0
O F:DMH563 3.3 16.8 1.0
C F:DMH563 3.4 16.4 1.0
O F:HOH2225 3.5 20.3 1.0
O F:ALA564 3.5 12.1 1.0
CB B:SER432 3.5 9.8 1.0
O F:HOH2109 3.9 15.6 1.0
CB F:DMH563 4.2 14.4 1.0
CE1 B:HIS363 4.2 2.8 1.0
CA F:DMH563 4.4 16.1 1.0
CG B:HIS363 4.4 5.5 1.0
CB F:ALA564 4.6 14.0 1.0
CA B:SER432 4.9 8.4 1.0
ND1 B:HIS363 5.0 3.0 1.0

Fluorine binding site 7 out of 12 in 1nkk

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Fluorine binding site 7 out of 12 in the Complex Structure of Hcmv Protease and A Peptidomimetic Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Complex Structure of Hcmv Protease and A Peptidomimetic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F1265

b:21.6
occ:1.00
 FB1 G:CFT1265 0.0 21.6 1.0
C1 G:CFT1265 1.3 20.8 1.0
FB2 G:CFT1265 2.1 21.7 1.0
FB3 G:CFT1265 2.1 23.1 1.0
C G:ALA1264 2.3 19.4 1.0
O G:ALA1264 2.7 19.8 1.0
CA G:ALA1264 2.8 19.8 1.0
CG C:ARG1165 3.1 16.5 1.0
CB C:ARG1165 3.3 15.8 1.0
N C:ARG1165 3.5 12.8 1.0
OG C:SER1132 3.5 18.4 1.0
NE C:ARG1165 3.7 21.3 1.0
N G:ALA1264 3.8 21.8 1.0
O G:DMH1263 3.8 21.7 1.0
CB G:ALA1264 3.9 19.4 1.0
CD C:ARG1165 3.9 20.0 1.0
CA C:ARG1165 3.9 14.4 1.0
C G:DMH1263 4.2 22.4 1.0
CB C:SER1132 4.3 14.7 1.0
C C:GLY1164 4.3 11.9 1.0
CA C:GLY1164 4.6 12.8 1.0
O C:VAL1163 4.6 13.9 1.0
NE2 C:HIS1063 4.8 3.5 1.0
CZ C:ARG1165 4.9 23.4 1.0

Fluorine binding site 8 out of 12 in 1nkk

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Fluorine binding site 8 out of 12 in the Complex Structure of Hcmv Protease and A Peptidomimetic Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Complex Structure of Hcmv Protease and A Peptidomimetic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F1265

b:21.7
occ:1.00
 FB2 G:CFT1265 0.0 21.7 1.0
C1 G:CFT1265 1.3 20.8 1.0
FB1 G:CFT1265 2.1 21.6 1.0
FB3 G:CFT1265 2.1 23.1 1.0
C G:ALA1264 2.4 19.4 1.0
O G:ALA1264 2.8 19.8 1.0
OG C:SER1132 3.0 18.4 1.0
CB C:SER1132 3.1 14.7 1.0
SG C:CYS1161 3.5 14.1 1.0
CA G:ALA1264 3.8 19.8 1.0
O C:VAL1163 3.9 13.9 1.0
NE2 C:HIS1063 3.9 3.5 1.0
CB C:CYS1161 3.9 10.9 1.0
N C:ARG1165 4.3 12.8 1.0
CD2 C:HIS1063 4.3 5.0 1.0
CA C:GLY1164 4.3 12.8 1.0
OD1 C:ASN1062 4.5 15.8 1.0
N G:ALA1264 4.5 21.8 1.0
CA C:SER1132 4.6 12.9 1.0
C C:GLY1164 4.7 11.9 1.0
C C:VAL1163 4.8 13.1 1.0
CB G:ALA1264 4.9 19.4 1.0
CG C:ARG1165 4.9 16.5 1.0
O C:HOH2136 5.0 5.2 1.0

Fluorine binding site 9 out of 12 in 1nkk

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Fluorine binding site 9 out of 12 in the Complex Structure of Hcmv Protease and A Peptidomimetic Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Complex Structure of Hcmv Protease and A Peptidomimetic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F1265

b:23.1
occ:1.00
 FB3 G:CFT1265 0.0 23.1 1.0
C1 G:CFT1265 1.3 20.8 1.0
FB1 G:CFT1265 2.1 21.6 1.0
FB2 G:CFT1265 2.1 21.7 1.0
C G:ALA1264 2.5 19.4 1.0
NE2 C:HIS1063 2.9 3.5 1.0
OG C:SER1132 3.0 18.4 1.0
CA G:ALA1264 3.1 19.8 1.0
CD2 C:HIS1063 3.1 5.0 1.0
N G:ALA1264 3.3 21.8 1.0
O G:DMH1263 3.4 21.7 1.0
C G:DMH1263 3.4 22.4 1.0
O G:ALA1264 3.6 19.8 1.0
CB C:SER1132 3.9 14.7 1.0
CE1 C:HIS1063 4.2 4.2 1.0
CB G:DMH1263 4.3 21.8 1.0
CG C:HIS1063 4.4 4.1 1.0
CA G:DMH1263 4.5 22.2 1.0
CB G:ALA1264 4.5 19.4 1.0
NE C:ARG1165 4.8 21.3 1.0
CG C:ARG1165 4.9 16.5 1.0
ND1 C:HIS1063 5.0 1.4 1.0

Fluorine binding site 10 out of 12 in 1nkk

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Fluorine binding site 10 out of 12 in the Complex Structure of Hcmv Protease and A Peptidomimetic Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Complex Structure of Hcmv Protease and A Peptidomimetic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F1565

b:26.5
occ:1.00
 FB1 H:CFT1565 0.0 26.5 1.0
C1 H:CFT1565 1.3 23.2 1.0
FB2 H:CFT1565 2.1 25.1 1.0
FB3 H:CFT1565 2.1 23.3 1.0
C H:ALA1564 2.4 21.4 1.0
O H:ALA1564 2.7 21.6 1.0
CA H:ALA1564 3.1 22.2 1.0
CG D:ARG1465 3.1 22.6 1.0
N D:ARG1465 3.3 14.0 1.0
CB D:ARG1465 3.4 18.4 1.0
OG D:SER1432 3.6 20.6 1.0
CA D:ARG1465 3.8 15.7 1.0
N H:ALA1564 4.0 23.6 1.0
O D:HOH2177 4.1 21.6 1.0
C D:GLY1464 4.1 12.5 1.0
CD D:ARG1465 4.2 26.1 1.0
NE D:ARG1465 4.2 30.7 1.0
CB H:ALA1564 4.2 21.2 1.0
O H:DMH1563 4.3 22.8 1.0
CB D:SER1432 4.3 16.2 1.0
CA D:GLY1464 4.3 13.2 1.0
O D:VAL1463 4.4 13.0 1.0
C H:DMH1563 4.5 24.3 1.0
NE2 D:HIS1363 4.7 10.5 1.0

Reference:

R.Khayat, R.Batra, C.Qian, T.Halmos, M.Bailey, L.Tong. Structural and Biochemical Studies of Inhibitor Binding to Human Cytomegalovirus Protease Biochemistry V. 42 885 2003.
ISSN: ISSN 0006-2960
PubMed: 12549906
DOI: 10.1021/BI027045S
Page generated: Mon Jul 14 11:22:52 2025

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